NPASS Compound

Structure

NPC10846 OpenBabel06302215272D 28 30 0 0 1 0 0 0 0 0999 V2000 6.4067 1.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4286 1.6288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7594 2.3719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0684 3.3230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3993 4.0661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4212 3.8582 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7520 4.6013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1122 2.9071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6999 2.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1122 1.2891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1611 1.5981 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1633 1.6641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4540 0.8910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4540 0.8910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2531 1.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2531 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4540 3.3052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4540 3.3052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1611 2.5981 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1770 2.9808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9703 2.3720 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1441 1.1441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0351 1.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9877 0.1564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0523 -0.9986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8387 -0.5446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1195 0.6777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 28 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 19 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 19 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 15 16 1 6 0 0 0 15 22 1 0 0 0 0 16 17 2 0 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 19 18 1 1 0 0 0 20 21 2 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 1 0 0 0 25 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	384.27
Volume:	428.475
LogP:	5.917
LogD:	4.463
LogS:	-5.607
# Rotatable Bonds:	5
TPSA:	54.37
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.514
Synthetic Accessibility Score:	5.01
Fsp3:	0.68
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.648
MDCK Permeability:	2.2014150090399198e-05
Pgp-inhibitor:	0.916
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.268
20% Bioavailability (F20%):	0.968
30% Bioavailability (F30%):	0.12

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.073
Plasma Protein Binding (PPB):	96.90782928466797%
Volume Distribution (VD):	2.543
Pgp-substrate:	3.7383482456207275%

ADMET: Metabolism

CYP1A2-inhibitor:	0.66
CYP1A2-substrate:	0.213
CYP2C19-inhibitor:	0.745
CYP2C19-substrate:	0.736
CYP2C9-inhibitor:	0.662
CYP2C9-substrate:	0.153
CYP2D6-inhibitor:	0.539
CYP2D6-substrate:	0.041
CYP3A4-inhibitor:	0.899
CYP3A4-substrate:	0.35

ADMET: Excretion

Clearance (CL):	5.519
Half-life (T1/2):	0.055

ADMET: Toxicity

hERG Blockers:	0.044
Human Hepatotoxicity (H-HT):	0.273
Drug-inuced Liver Injury (DILI):	0.077
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.973
Skin Sensitization:	0.903
Carcinogencity:	0.791
Eye Corrosion:	0.042
Eye Irritation:	0.152
Respiratory Toxicity:	0.982

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC10846

Natural Product ID:	NPC10846
*Common Name:**	YVGINRGIDPTPQF-PUIZSHONSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YVGINRGIDPTPQF-PUIZSHONSA-N
Standard InCHI:	InChI=1S/C25H36O3/c1-16(2)7-6-8-17(3)19-11-12-24(4)13-21-23(22(27)14-25(21,5)28)18(15-26)9-10-20(19)24/h7,9,11,15,17,20-21,23,28H,6,8,10,12-14H2,1-5H3/b18-9-/t17-,20-,21-,23+,24+,25+/m0/s1
SMILES:	CC(=CCC[C@H](C)C1=CC[C@]2(C)C[C@H]3[C@@H](C(=CC[C@@H]12)C=O)C(=O)C[C@@]3(C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101201587
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001552] Sesterterpenoids [CHEMONTID:0002882] Ophiobolane sesterterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15684	Cochliobolus heterostrophus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10395513]
NPO15783	Stemona phyllantha	Species	Stemonaceae	Eukaryota	n.a.	tuberous root	n.a.	PMID[21902195]
NPO15783	Stemona phyllantha	Species	Stemonaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21902195]
NPO13275	Centaurea scabiosa	Species	Asteraceae	Eukaryota	n.a.	fruit	n.a.	PMID[22396124]
NPO2990	Solenostemon scutellarioides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15783	Stemona phyllantha	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12794	Hypericum pseudopetiolatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15684	Cochliobolus heterostrophus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2613	Artemisia ordosica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5756	Amanita abrupta	Species	Amanitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16542	Aloe rupestris	Species	Xanthorrhoeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5119.2	Pseudomonas chlororaphis subsp. aureofaciens	Subspecies	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15571	Iphiona pinnatisecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11651	Parsonsia heterophylla	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16867	Bursera permollis	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13275	Centaurea scabiosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC10846 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	201
0.1-0.2	1729
0.2-0.3	8685
0.3-0.4	15080
0.4-0.5	8592
0.5-0.6	6189
0.6-0.7	2004
0.7-0.8	191
0.8-0.85	15
0.85-0.9	5
0.9-0.95	5
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC10846 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	190
0.1-0.2	2513
0.2-0.3	4219
0.3-0.4	1571
0.4-0.5	321
0.5-0.6	179
0.6-0.7	149
0.7-0.8	8
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data